Homology-based loop modeling yields more complete crystallographic protein structures

IUCrJ

van Beusekom, B.¹ 

[1] Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands

关键词: LOOP BUILDING;    STRUCTURAL RE-BUILDING;    PDB-REDO;    MODEL COMPLETION;    CRYSTALLOGRAPHY;   

DOI  :  10.1107/S2052252518010552

学科分类：数学（综合）

来源: International Union of Crystallography

【 摘 要 】

Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and `graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.

【 授权许可】

CC BY